[Coral-List] coral genome
Tonya Shearer
tlsnell at buffalo.edu
Wed Sep 17 16:07:32 EDT 2003
Having sequenced DNA from many Caribbean scleractinian
species, I thought I would add a couple of comments. One
consideration when choosing a species is the availability of
zooxanthella-free tissue (ideally sperm). In my experience, DNA
from the zoox is often amplified (and subsequently sequenced) in
addition to the coral DNA, unless the tissue is free from zoox or the
primers are specific to cnidarians. Obtaining gametes from
broadcasting species is relatively easy, whereas brooded larvae
often already have zoox from the maternal colony. I'm not sure
how easy it is to get sperm from brooding species.
My personal preference is for a Porites species, one because I
have developed microsatellites for P. astreoides (unfortunately a
brooder), and two, because there are several representatives in
the Indo-Pacific and Caribbean. Thus this genome can be used
as a model for efficiently developing genetic markers for several
Porites species. Three, conducting molecular analysis on Porites
(at least Caribbean species) is very easy = high amplification and
sequencing success (not the case for some other species).
Finally, as brooders that release larvae multiple times throughout
the year, molecular biologists can take advantage of breeding
experiments without having to hope for good weather conditions
on the couple of evenings of mass spawning.
I have also developed microsatellites for Montastraea cavernosa.
Although technically easier to work with as far as eliminating the
concern for zoox contamination by using sperm, I think
sequencing a Montastraea genome would on the whole, be less
useful for molecular biologists than a species from a more
widespread genus.
No matter which species is chosen, this information is extremely
useful for those of us that are interested in the genetic structure
and gene flow (larval transport) of coral species. For those of you
that don't know the struggles of doing molecular work on corals,
standard molecular markers used for population genetics on
other organisms (mitochondrial genes) cannot be used in corals
due to a slow rate of evolution in the mitochondrial genome.
Therefore we have to develop other markers, which can take
years. Having a model genome available to develop these
markers will save time, money and the sanity of those doing the
work.
Tonya (Snell) Shearer
tlsnell at buffalo.edu
109 Cooke Hall
University at Buffalo
Buffalo, NY 14260
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